The purpose of this research is to determine the relative rates of emergence of HIV-1 resistance and to compare changes in plasma HIV RNA levels and CD4+ cell counts in a sample of patients with CD+ cell counts < 100/mm3 who are enrolled in CPCRA 042/CTN 102. This is a multicenter resistance substudy of the NvR Protocol (CPCRA 042/CTN 102), an open-label, randomized comparison of nelfinavir (NFV) and ritonavir (RTV)/indinavir (IDV). RTV/IDV refers to the group of participants initially assigned to RTV, some of whom may have switched to IDV due to the development of significant intolerance to RTV. Laboratory specimens obtained for this substudy will be analyzed blinded to the treatment assignment. Patients will be enrolled over a 12-month period and followed for a minimum of 12 months to a common closing date, determined by the main NvR study, CPCRA 042/CTN 102. The average follow up is estimated to be 18 months. The sample size will include 600 patients, 400 from CPCRA sites and 200 from CTN sites, will be enrolled in the substudy. Viral loads will be determined on all patients at baseline and during follow up. Initially, specimens for 50 randomly chosen patients in the group originally assigned RTV will be identified for resistance testing. Of this group, specimens for those who have received RTV/IDV for more than 1 month will be analyzed for genotypic resistance to obtain an estimate of the rate o resistance development and to estimate the risk of disease progression associated with resistance to RTV/IDV.